Observing Microbial Processes at the Microscale with In Situ Technology

Marine microbes are key drivers of biogeochemical transformations within the world’s oceans. Although seawater appears uniform at scales that humans often interact with and sample, the world that marine microbes inhabit is heterogeneous, with numerous biological and physical processes giving rise to resource hotspots. While the impact of this microscale heterogeneity has been investigated in the laboratory and theoretical models, ecologists have lacked tools to interrogate microscale processes in the environment. Within this thesis I introduce three new technologies that enable interrogation of microbial processes at the microscale in natural marine communities. The IFCB-Sorter acquires images and sorts individual phytoplankton cells, allowing studies exploring connections between the forms present in the plankton and genetic variability at the single-cell level. The In Situ Chemotaxis Assay (ISCA) is a field-going microfluidic device designed to probe the role of microbial motility in aquatic environments. Finally, the Millifluidic In Situ Enrichment (MISE) is an instrument that enables the study of rapid shifts in gene expression that permit microbes to exploit chemical hotspots. These instruments allow examination of microbial life at the microscale and empower ecologists to develop a more holistic understanding of how interactions at the scale of microbes impact processes in marine ecosystems.